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RESEARCH ARTICLE

Transcriptional Responses and Gentiopicroside Biosynthesis in Methyl Jasmonate-Treated Gentiana macrophylla Seedlings Xiaoyan Cao1, Xiaorong Guo1, Xinbing Yang1, Huaiqin Wang1, Wenping Hua2, Yihan He1, Jiefang Kang1*, Zhezhi Wang1*

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1 Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi’an, China, 2 Department of Biological Science and Technology, Shaanxi XueQian Normal University, Xi’an, China * [email protected] (JK); [email protected] (ZW)

Abstract OPEN ACCESS Citation: Cao X, Guo X, Yang X, Wang H, Hua W, He Y, et al. (2016) Transcriptional Responses and Gentiopicroside Biosynthesis in Methyl JasmonateTreated Gentiana macrophylla Seedlings. PLoS ONE 11(11): e0166493. doi:10.1371/journal. pone.0166493 Editor: Baohong Zhang, East Carolina University, UNITED STATES Received: August 24, 2016 Accepted: October 28, 2016 Published: November 16, 2016 Copyright: © 2016 Cao et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: This work was funded by the Natural Science Foundation of Shaanxi Province, China (2014JQ3107) and the Fundamental Research Funds for the Central Universities (GK201302043). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Gentiana macrophylla, a medicinal plant with significant pharmacological properties, contains the bioactive compound gentiopicroside. Methyl jasmonate (MeJA) is an effective elicitor for enhancing the production of such compounds. However, little is known about MeJAmediated biosynthesis of gentiopicroside. We investigated this phenomenon as well as gene expression profiles to determine the molecular mechanisms for MeJA-mediated gentiopicroside biosynthesis and regulation in G. macrophylla. Our HPLC results showed that Gentiana macrophylla seedlings exposed to MeJA had significantly higher concentrations of gentiopicroside when compared with control plants. We used RNA sequencing to compare transcriptional profiles in seedlings treated for 5 d with either 0 μmol L-1 MeJA (C) or 250 μmol L-1 MeJA (M5) and detected differentially expressed genes (DEGs). In total, 77,482 unique sequences were obtained from approximately 34 million reads. Of these, 48,466 (57.46%) sequences were annotated based on BLASTs performed against public databases. We identified 5,206 DEGs between the C and M5 samples, including genes related to the α-lenolenic acid degradation pathway, JA signaling pathway, and gentiopicroside biosynthesis. Expression of numerous enzyme genes in the glycolysis pathway was significantly up-regulated. Many genes encoding transcription factors (e.g. ERF, bHLH, MYB, and WRKY) also responded to MeJA elicitation. Rapid acceleration of the glycolysis pathway that supplies precursors for IPP biosynthesis and up-regulates the expression of enzyme genes in that IPP pathway are probably most responsible for MeJA stimulation of gentiopicroside synthesis. Our qRT-PCR results showed that the expression profiles of 12 gentiopicroside biosynthesis genes were consistent with the RNA-Seq data. These results increase our understanding about how the gentiopicroside biosynthesis pathway in G. macrophylla responds to MeJA.

PLOS ONE | DOI:10.1371/journal.pone.0166493 November 16, 2016

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Gentiopicroside Biosynthesis and Methyl Jasmonate-Treated Gentiana macrophylla Seedlings

Competing Interests: The authors have declared that no competing interests exist.

Introduction The plant hormone methyl jasmonate (MeJA) is an efficient elicitor of secondary metabolite production [1]. Those metabolites include flavonoids, phenolic and polyphenolic compounds, terpenoids, and alkaloids. Such bioactive compounds in plants represent valuable and unique resources for food additives, cosmetics, and pharmaceutical drugs [2]. Treating plants with MeJA can trigger the biosynthesis of terpenoids, alkaloids, phenylpropanoids, and phytoalexins through extensive transcriptional reprogramming of their metabolism [1, 3–7]. Gentiana macrophylla Pall (family Gentianaceae) is a perennial medicinal plant prescribed in China since ancient times to treat arthralgia, stroke, hemiplegia, pain, jaundice, infantile malnutrition, and osteoarthritis [8]. Its dried roots are officially listed in the Chinese Pharmacopoeia under the name Radix Gentianae Macrophyllae (Qin-jiao in Chinese) and are frequently used to dispel rheumatism and ease pain [9]. Gentiopicroside, an abundant and indicative ingredient in Qin-jiao, is the most important active component of total secoiridoid glycosides and has significant anti-inflammatory, analgesic, and antibacterial properties, as well as biological activity for treating osteoarthritis and strengthening gastric motility [10,11]. Although levels of gentiopicroside in Qin-jiao are influenced by soil elements and fertilization [12,13], the effect of MeJA in regulating those concentration has not been investigated. Gentiopicroside is synthesized via the secoiridoid pathway. This pathway has been well studied and reviewed in Catharanthus roseus [14,15], and most steps have been identified. In the first step within higher plants, isopentenyl diphosphate (IPP), a precursor of terpenoids, is formed through either the plastidial 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway or the cytosolic mevalonic acid (MVA) pathway. The allylic isomer of IPP, dimethylallyl diphosphate, reacts with one IPP in a head-to-tail fashion to form geranyl diphosphate, which is then catalyzed and converted into geraniol. The secoiridoid pathway starts with geraniol and proceeds through a series of reaction steps leading to the formation of secologanin [15]. Ultimately, secologanin is converted into gentiopicroside and other secoiridoids through several currently unknown steps [16]. In contrast to conventional methods, such as single gene cloning and DNA microarrays, that yield a limited amount of genetic information, RNA-seq is powerful tool for analyzing differential gene expression with high resolution at the whole-genome level [17,18]. In particular, transcriptome analysis can reveal relationships between plant gene expression and phenotype [19–21]. No previous regulatory mechanisms for gentiopicroside biosynthesis have been reported for G. macrophylla. However, de novo analysis using next-generation sequencing technologies can provide a robust platform for elucidating the mechanisms that might influence the accumulation of gentiopicroside in that species. Because data are lacking for the means by which gentiopicroside production in G. macrophylla is modulated by MeJA, we monitored concentrations of that compound in MeJAtreated seedlings. Methyl jasmonate stimulates gentiopicroside biosynthesis. Therefore, RNAseq can be used to analyze differential gene expression over time in MeJA-treated plants versus the control. In general, applications of MeJA trigger profound transcriptional reprogramming in plant cells to manipulate the machinery that controls a wide range of metabolite biosynthesis via interplay of both positive and negative regulators [22]. Improving our understanding of the events between MeJA application and gentiopicroside accumulation will be useful for developing strategies to enhance production in G. macrophylla. Therefore, our objective here was to identify the relevant metabolic pathways for major MeJA-responsive genes and decipher the molecular mechanism by which MeJA stimulates yields.


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Materials and Methods Plant growth conditions and treatments Seeds of Gentiana macrophylla were collected from the cultivation base of our lab, which is located in Taibai county, Shaanxi province, China. They were surface-sterilized with 2% sodium hypochlorite for 9 min, followed by five rinses with distilled water. After being kept in the dark for 2 d, they were germinated on culture dishes containing an MS solid medium (16-h photoperiod, 20˚C). One-month-old seedlings were transferred to either a fresh MS solid medium (control; 0 μmol L-1 MeJA) or an MS medium supplemented with 250 μmol L-1 MeJA. Whole seedling samples were collected after 1, 3, 5, 7, 9, and 11 d of treatment and dried to constant weight at 40˚C for the determination of gentiopicroside contents. The experiments were performed in three individual biological replications and every treatment contained more than 30 seedlings.

Measurements of gentiopicroside Gentiopicroside concentrations were determined via High Performance Liquid Chromatography (HPLC). All sample solutions and stock solutions of gentiopicroside were prepared as we have described before [23]. Chromatographic separations were conducted with a C18 column (250 × 4.6 mm, 5 μm particle size; Agilent Technologies Inc., USA) on an Agilent 1260 Infinity LC system, using a solvent system comprising 70% ddH2O (A) and 30% methanol (B). The flow rate was adjusted to 0.8 mL min-1 and the detection wavelength was 245 nm. All separations were performed at 25˚C.

RNA isolation Total RNA was isolated using TRIzol1 Reagent (Invitrogen, USA) according to the manufacturer’s protocol. Quality of the RNA was assessed on agarose gels and the concentration was determined with a NanoDrop ND2000 Spectrophotometer (NanoDrop Technologies Inc., USA).

cDNA library construction and sequencing Two cDNA libraries—C (control) and M5 (MeJA treatment for 5 d)—were generated using mRNA-Seq Sample Prep Kits (Illumina, USA) according to the manufacturer’s instructions. Magnetic beads containing poly-T molecules were used to isolate the poly(A) mRNA from 20 μg of total RNA. Following purification, the samples were fragmented into small pieces using divalent cations at 94˚C for 5 min, then converted into first- and second-strand cDNA with a SuperScript double-stranded cDNA synthesis kit (Invitrogen). The synthesized cDNA was subject to end repair and adenylation of the 3’ ends and purified using a QIAquick PCR Purification Kit (QIAGEN, Germany). Afterward, Illumina paired-end adapters were ligated to the resulting cDNA fragments. Each cDNA library was constructed with an insert size of 200 bp. After quality was verified on an Agilent 2100 Bioanalyzer, deep-sequencing was performed with an Illumina HiSeq4000. In all, 150 bp paired-end reads were generated.

De novo assembly and gene annotation Raw reads were filtered by the Illumina pipeline prior to assembly. We removed any reads that showed adapter contamination or for which more than 20% of the bases had quality values 10 or more than 5% were unknown nucleotides. The high quality clean reads were then randomly clipped into overlapping K-mers with default K = 25 for assembly with the Trinity, a short-reads assembling program [24]. The resulting sequences, termed unigenes, from each sample’s assembly were further processed for sequence-splicing and removal of all redundancy


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to acquire non-redundant unigenes that were as long as possible. Finally, Blast X alignments were made (E-values